MolNFT v1 · #169102 · protein
Structure of human plasma factor xiia in complex with (2S)-1-(N,3- dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3- oxazol-2-yl]-N-[(thiophen-2-YL)METHYL]PIPERAZINE-2-carboxamide (compound 8H)
6X0T · Coagulation factor XII: “Structure of human plasma factor xiia in complex with (2S)-1-(N,3…”. X-ray diffraction, 2 ligands (UJ7, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #169102 on GenesisL1: 3D structure, binding sites…
- PDB
- 6X0T
- Type
- protein
- Length
- 719 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XII
- EC
- 3.4.21.38
- UniProt
- P00748
- Ligands
- UJ7, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XII (EC 3.4.21.38) | protein | 241 | 12% helix, 34% strand | P00748 |
| B | Coagulation factor XII (EC 3.4.21.38) | protein | 238 | 11% helix, 35% strand | P00748 |
| C | Coagulation factor XII (EC 3.4.21.38) | protein | 240 | 12% helix, 35% strand | P00748 |
Ligands and binding sites
- UJ7 · (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.75 | 0.78 | 89 | empty |
| 2 | 124 | 0.42 | 0.76 | 30 | UJ7 |
| 3 | 110 | 0.42 | 0.77 | 25 | UJ7 |
| 4 | 99 | 0.41 | 0.77 | 27 | UJ7 |
Interfaces
3 interfaces between chains.
- B–C · 274 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00748
- Elsewhere: RCSB PDB 6X0T · PDBe 6X0T · UniProt P00748
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